Abstract: This invention provides a computer based method for preparing a stem cell factor (SCF) analog comprising the steps of: (a) providing computer expression of the three dimensional structure of an SCF molecule using its crystal structure; (b) selecting from the computer expression of step (a) at least one site on the SCF molecule for alteration; (c) preparing a SCF molecule having an alteration at said at least one selected site; and (d) optionally, testing the SCF molecule for a desired characteristic. This invention also provides SCF analogs and SCF ligand analogs prepared according to the above-described method. Compositions comprising SCF analogs or SCF ligand analogs prepared according to the above-described method effective to treat a subject and a pharmaceutically acceptable carrier are provided, as are methods of treating a subject comprising administration of pharmaceutical compositions comprising the prepared SCF analogs and SCF ligand analogs prepared by the described methods.